It is correct for there to be no residue RYA in GLYCAM_06j-1.prep.  To
use the name RYA makes logical sense, so I understand why it was
chosen, but it technically isn't the correct name to use.

The current GLYCAM residue naming convention has numerous limitations,
and you have just encountered one.  A new naming convention was
proposed in the article at the link just below.  We want to switch to
this, or some other, more flexible naming convention, but doing so
will not be a trivial task and must be done with great care and
attention to detail.
http://glycob.oxfordjournals.org/content/18/6/426.full.pdf+html
(proposed new naming)

So, Anu, I understand that your choice of the name RYA signifies the
fact that an SO3 is attached at positions 2 and 6, with another
monosaccharide at position 4.  However, our naming doesn't recognize
an 'N' as an attachment position in that sense.  The naming, at least
thus far, has only considered open valences at hydroxyl oxygens.  So
there is no definition at all for attachments at "position 2" of a
GlcNAc or similar residue - note that there is also no residue called
'2YA' in the prep file.

BTW, the RYA in Table 4 on our naming page (glycam.org/naming) is a
typo that has been present, but not noticed, since around the release
of GLYCAM-04.

To other Woods/GLYCAM folks... We *could* adopt this naming, allowing
N to be an open valence.  So, 2YA would be -2DGlcpNa1- with an open
valence at the N, which is at the 2 position.  That might simplify
things in the meantime.  We might not be able to generate all the
NAc-relevant residues in the database, but there would be names for
many of them.  Also, this still doesn't give us a plain GlcpN, but we
don't have that anyway.  It also might allow things to be attached
there that should not be.  We could check to see if a lack of ff
parameters would keep this from being a problem in a simulation.

Back to everyone:  In the background, the builder currently calls the
files xYS for alpha and xYs for beta (for a lack of an official naming
convention).  So, 4YS is -4DGlcpNSa1- and so forth.  I can post those
prep files for now in the "Special Releases" section.  I think that is
all Anu needs.  We can always update the names and such later as
desired.


-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA